Version 2.1.3

OEChem TK 2.1.3

New features

Warning

The standard InChI format includes chemical normalization activity that results in round-trip structure alterations to a very high percentage of structures when unnormalized or when arbitrary input chemistry is used. Even the output of OEMolToInChI, which generates a nonstandard InChI and attempts to minimize structure normalizations, results in many changes to input chemical structures.

  • OEInChIOptions now supports relative stereo and racemic stereo InChI output as well as control of the timeout condition.
  • The default output flavor for writing InChI or InChIKey via OEWriteMolecule has been changed to include the molecule title as well as the InChI information to synchronize behavior with other output formats. Since the InChI identifiers never include white space, there should be no ambiguity for separating the InChI information from the title. If there are third-party readers that have problems with the title, the following output flavor bits are now available to control whether the title is added to the output: OEOFlavor_INCHI_Title and OEOFlavor_INCHIKEY_Title.
  • An overload of OEShortestPath has been added to take an atom predicate and return the shortest path between atoms that are not excluded by the predicate.

Minor bug fixes

OESystem TK 2.1.3

New features

  • A new parameter has been added to the constructor of OEDots that enables changing the “processed” label in the output lines.

Minor bug fixes

  • The function OEGetTag and method OEBase.GetData could segfault when called with a null char * argument in C++ or with an empty argument in the wrapped languages. These have been fixed.

OEBio TK 2.1.3

New features

Minor bug fixes

  • GetGroups no longer crashes on Windows in cases where no alternate location group exists.
  • Calling the function OEBuildUnitCell on protein molecules had previously consumed large amounts of memory and, as a result, would often crash. This issue has been addressed, and the performance of the function has been improved for molecules of small or medium size.
  • Interaction perception for anionic carbonyl groups has been fixed.
  • OEIsValidActiveSite now takes into account the non-default parameter ligand component type.

Documentation changes

  • An example in Preparing a Protein has been modified to work properly when splitting a ligand from a binding site other than the first one.

OEGrid TK 1.6.0

Minor bug fixes

  • OEMaskGridByMolecule no longer segfaults for an empty molecule or for a molecule without 2D coordinates. It now throws a warning and returns false.
  • On Windows, UTF8 file and directory names are now correctly supported for toolkit file I/O operations.

Java-specific changes

Documentation changes